We've rented a pontoon in years' past and we've also taken our own boat out, putting in at the St. Andrews State Park ramp. Either way, being your own captain permits a more personalized pace and provides for plenty of room for snacks and drinks. And don't be intimidated - boating on the bay is not difficult in good weather. A half-day rental may be long enough, but a full day is only about $80 more. Scotty's has good rates (but no web site). As others have said, be prepared for no potties on the island.
Plan your trip early in your stay and make a reservation if your renting a boat. This year we reserved a pontoon for Friday afternoon. Turned out we had to cancel because of thunderstorms. Wish we had booked for Tuesday or Wednesday instead!